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obophenotype / upheno

The Unified Phenotype Ontology (uPheno) integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.
https://obophenotype.github.io/upheno/
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Relate phenotypes to traits #716

Open cmungall opened 3 years ago

cmungall commented 3 years ago

We have species-neutral traits in OBA (all kingdoms) and TO (plant traits). OBA can be mapped to EFO, ATO, VT

What should the relationship be between OBA and upheno?

matentzn commented 3 years ago

I think we have been stuck on this issue for a long time, I would also like to progress on it. Can we collect some concrete use cases?

Given that OBA definitions are like:

quality and inheres in some gastrulation

and as the has part buffer in phenotype ontologies is there to stay, why don't we simply redefine has part as has qualified trait (or whatever relation), and then say that a phenotype is defined as something that has a (qualified) trait, where qualified in this case means "abnormal", "normal" etc? This would be quite practical (we dont need to discuss the tiring "is a phenotype a subclass of a trait) discussion, and we could simply define grouping classes and connect the two worlds by using that new relation? Just a thought.